What are the best practices and tools to increase security of the mnemonic/seed phrase? For example I can imagine building a deterministic permutation in order to create a trapdoor mnemonic. Same could be done by using non-standard derivation path.

Full-time builder. Pimlico | @33bits | farcaster-solidity. Zero-knowledge and asynchronous transactions evangelist.

The Art of Exchange, The Science of Payments

Co-founder, Cosmos. CEO, Informal Systems. 

Not sure I think probably under supported I’m generally disappointed in the lack of support for eg setting custom bip32 paths this is always a big blocker for me with metamask. Keplr (cosmos) supports that. Not sure about passphrase support though the the ledger devices do support it

Exactly, that's what I was looking for! And what is the state of modern wallet support? I've seen an option to enter a passphrase in Ledger/MetaMask/Coinbase wallet/etc.